Programs and Utilities
installed for the purposes of Bioinfo3D group development and research.
 

• For operating instructions you can either run the program for "Usage Help" (type the program name and press the Enter) or see "Documentation".
• If you can't run the program from command prompt try to add the location (as it appears in the table) before the program name (example: to run the 'rmsd_calc' type utils/rmsd_calc and Enter) or add the 'location' to the path variable in .cshrc file.
• !!! the starting path for all programs is /home/silly6/mol/

Program Name	Description	Location (/home/silly6/mol/)
dssp	Secondary structure assignment.	software/DSSP2000/
getLocalPDB.pl	Finds pdb from local database	utils/
getChain	Gets specified chain from pdb file	utils/get_chain/
pdb_trans	trasforms molecule of pdbfile by given transfomation (rotate and translate)	utils/pdb_trans.Linux/
vmd	Visual Molecular Dynamics Documentation	software/vmd/
rasmol_  16BIT or 32BIT	Molecular Visualization Documentation	utils/Rasmol/
runMSPoints	finds Connolly points (surface dots)	software/CP/SurfacePointsLinux
runShuoPoints	finds Shuo points	software/CP/SurfacePointsLinux
shuo2pdb	converts shuo file format to pdb format	software/CP/SurfacePointsLinux
rmsd_calc	calculates transformation that minimizes the RMSD between two protein structures (proteins should have the same number of amino acids)	utils/
blast	Performs pairwise sequence alignment of a fasta format sequence against a sequence database. On line tutorial	blastIrix/,blastLinux/
clustalx	Performs multiple sequence alignment or profile alignment. On line tutorial	ClustalxIRIX/,ClustalxLINUX
cdr.Linux	Detects antibody's CDR loops.	utils/cdr